mutM:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
/Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php
Convert to gbrowse_img.php extension.
Line 75: Line 75:
82.08 minutes 
82.08 minutes 
|
|
MG1655: 3809175..3808366<br />{{GBrowseFigureByCoord|3808366|3809175|ecoli|MG1655}}
MG1655: 3809175..3808366<br /><gbrowseImage>
name=NC_000913:3808366..3809175
source=ecoli
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10329 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10329 EcoCyc]
Line 89: Line 94:


|
|
NC_012967: 3749507..3748698<br />{{GBrowseFigureByCoord|3748698|3749507|REL606|NC_012967}}
NC_012967: 3749507..3748698<br /><gbrowseImage>
name=NC_012967:3748698..3749507
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|3748698|3749507|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3748698|3749507|GBrowse (REL606)}}
Line 100: Line 110:


|
|
NC_012759: 3696692..3697501<br />{{GBrowseFigureByCoord|3696692|3697501|BW2952|NC_012759}}
NC_012759: 3696692..3697501<br /><gbrowseImage>
name=NC_012759:3696692..3697501
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|BW2952|012759|3696692|NC_3697501|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|012759|3696692|NC_3697501|GBrowse (BW2952)}}
Line 111: Line 126:
&nbsp;
&nbsp;
|
|
W3110: 3829263..3830072<br />{{GBrowseFigureByCoord|3829263|3830072|ecoli_W3110|W3110}}
W3110: 3829263..3830072<br /><gbrowseImage>
name=AC_000091:3829263..3830072
source=ecoli_W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3828263|3831072|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|AC_000091|3828263|3831072|GBrowse(W3110)}}  
Line 122: Line 142:


|
|
DH10B: 3906752..3905943<br />{{GBrowseFigureByCoord|3905943|3906752|ecoli_DH10B|DH10B}}
DH10B: 3906752..3905943<br /><gbrowseImage>
name=NC_010473:3905943..3906752
source=ecoli_DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3904325|3908370|GBrowse(DH10B)}}
{{GBrowseLink|ecoli_DH10B|NC_010473|3904325|3908370|GBrowse(DH10B)}}

Revision as of 21:19, 26 July 2010

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

mutM

Mnemonic

Mutator

Synonyms

ECK3625, b3635, JW3610, fpg[1]

edit table


Notes

Location(s) and DNA Sequence

[back to top]


See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

82.08 minutes 

MG1655: 3809175..3808366
<gbrowseImage> name=NC_000913:3808366..3809175 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3749507..3748698
<gbrowseImage> name=NC_012967:3748698..3749507 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3696692..3697501
<gbrowseImage> name=NC_012759:3696692..3697501 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3829263..3830072
<gbrowseImage> name=AC_000091:3829263..3830072 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3906752..3905943
<gbrowseImage> name=NC_010473:3905943..3906752 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3808369

Edman degradation

PMID:3319582[2]


edit table


Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔmutM (Keio:JW3610)

deletion

deletion

PMID:16738554[3]

Shigen

mutM::Tn5KAN

PMID:12519969[4]

ASAP

At position 312 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB21352

mutM::Tn5KAN

PMID:12519969[4]

ASAP

At position 312 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB21353

mutMK218T

K218T

Slight increase of substrate affinity and decrease of activity

seeded from UniProt:P05523

mutME174Q

E174Q

Strong decrease of glycosylase activity; slight decrease of AP lyase activity

seeded from UniProt:P05523

mutME3Q

E3Q

Strong decrease of glycosylase activity; slight decrease of AP lyase activity

seeded from UniProt:P05523

mutME6Q

E6Q

Decrease of glycosylase activity; no effect on AP lyase activity

seeded from UniProt:P05523

mutMH90A

H90A

Increase of substrate affinity and decrease of activity

seeded from UniProt:P05523

mutMD107N

D107N

No effect on glycosylase and AP lyase activity

seeded from UniProt:P05523

mutMR109A

R109A

Over 100-fold decrease of activity

seeded from UniProt:P05523

mutMR110A

R110A

Over 100-fold increase of substrate affinity and decrease of activity

seeded from UniProt:P05523

mutME132Q

E132Q

Decrease of glycosylase activity; slight decrease of AP lyase activity

seeded from UniProt:P05523

mutMD160N

D160N

No effect on glycosylase and AP lyase activity

seeded from UniProt:P05523

mutM102::kan

PMID:8676878[5]

CGSC:67990

mutM103::mini-Tn10

PMID:8676878[5]

CGSC:67993


edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3610

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCCTGAATTACCCGAAGTTGA

Primer 2:CCtTTCTGGCACTGCCGACAATA

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[7]

est. P1 cotransduction: % [8]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[7]

est. P1 cotransduction: 50% [8]

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10329

EchoBASE (EcoliWiki Page)

EchoBASE:EB0325

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3635

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4459

EcoGene (EcoliWiki Page)

EcoGene:EG10329

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:MUTM

CGSC (EcoliWiki Page)

CGSC:18133

ASAP (EcoliWikiPage)

ASAP:ABE-0011877


edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Boiteux, S et al. (1987) Formamidopyrimidine-DNA glycosylase of Escherichia coli: cloning and sequencing of the fpg structural gene and overproduction of the protein. EMBO J. 6 3177-83 PubMed
  3. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  4. ↑ 4.0 4.1 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  5. ↑ 5.0 5.1 Bridges, BA et al. (1996) Effect of mutY and mutM/fpg-1 mutations on starvation-associated mutation in Escherichia coli: implications for the role of 7,8-dihydro-8-oxoguanine. Mol. Gen. Genet. 251 352-7 PubMed
  6. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=mutM:Gene&oldid=1178086"